Freesurfer September 2020

freesurfer@nmr.mgh.harvard.edu

111 participants
165 discussions

brainGraph (graph theory analysis in R) major release v3.0.0
by Chris Watson 30 Sep '20

30 Sep '20

External Email - Use Caution Dear Freesurfer users, (apologies for cross-posting) I am pleased to announce the 3nd major release of my R package for graph theory analysis of brain MRI data, "brainGraph". The main page on CRAN is at: https://cran.r-project.org/web/packages/brainGraph/index.html The GitHub repository is at: https://github.com/cwatson/brainGraph *Installation* The latest version is already on CRAN for Linux distributions, and should be for Windows and Mac OS X soon. To install directly from CRAN: > install.packages('brainGraph') In the meantime (and for development versions), you may install from GitHub using the R package "devtools": > devtools::install_github('cwatson/brainGraph') *Getting help* The User Guide can be found at: my GitHub Pages site (PDF warning) <https://cwatson.github.io/files/brainGraph_UserGuide.pdf>. Chapter 4 gives a general Overview, and Chapter 5 has some basic details for getting started. Chapters 6 and 7 provide code and details for structural covariance and single-subject networks, respectively. You may also get help by opening an Issue <https://github.com/cwatson/brainGraph/issues> on the GitHub repository, or you may join the Google Group <https://groups.google.com/forum/?hl=en#%21forum/brainGraph-help>. *New features* You can find the release notes/changelog in NEWS.md, at: https://github.com/cwatson/brainGraph/blob/master/NEWS.md There are too many differences to list here, but the most significant new feature is related to GLM-based analyses (including for Multi-threshold Permutation Correction, Network Based Statistic, and mediation analysis). They are now significantly faster, and (in certain situations) is faster than other solutions in R. Please let me know if you have any issues, bug reports, feature requests, etc. Chris Watson

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Regressing out gender
by WON JONG CHWA 30 Sep '20

30 Sep '20

External Email - Use Caution Hello, I am currently attempting a paired t-test of subjects between two time points, regressing out the effects of age and gender. I am currently running the paired analysis tutorial, and have done the step of computing the differences between pairs using mris_preproc --paired-diff. However, I am having trouble with the FSGD and contrast files. Currently, this is my FSGD file: GroupDescriptorFile 1 Class M Class F Variables Age Input subject1pair M 80 Input subject2pair F 82 ... I am not sure how to make the contrast file for this, I would like to answer the question of " does the mean paired difference differ from 0, regressing out the effect of age and gender?" Any assistance would be greatly appreciated. William

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extract morphology data
by 姜黎黎 29 Sep '20

29 Sep '20

External Email - Use Caution Hello, I am Lili Jiang from Institute of Psychology Chinese Academy of Sciences. I used freesurfer to do MRI data analysis. When I used mri_preproc to extract morphology data, I always got log file writing 'Reading source surface reg ~/sub001/surf/rh.fsaverage5.sphere.reg No such file or directory mri_surf2surf: could not read surface ~/sub001/surf/rh.fsaverage6.sphere.reg No such file or directory'. It seemed that mri_surf2surf loaded by mris_preproc always wanted to load reg file with 'fsaverage5'. But when I extrated morphology data in the resolution of fsaverage, then everything went well. Could you tell me what's wrong with this? ps. I just upgraded freesurfer to v6.0 last summer. Best, Lili

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LGI value extraction
by 祝菲 29 Sep '20

29 Sep '20

External Email - Use Caution Dear expert, I have used freesurfer v6.0 to calculate local Gyrification index ( LGI ). And I have output the file named lh.pial_lgi and extracted the value of LGI by using the following command: > mris_anatomical_stats -a ${SUBJECTS_DIR}/S005/label/lh.aparc.annot -t pial_lgi -f ${SUBJECTS_DIR}/S005/stats/lh.aparc_lgi.stats S005 lh > aparcstats2table --subjects S005 --hemi lh --meas thickness --skip —parc aparc_lgi --tablefile result_lgi_lh.txt However, I found that the header of the output result showed the “thickness" instead of “LGI". Does this “thickness" represent the index of “LGI"? I have attached the result of one sample in the attachment. Thank you again for taking your precious time to solve my problem！ kind regards zhu fei

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preproc-sess - motion correction problem
by Nasr, Shahin,Ph.D. 29 Sep '20

29 Sep '20

Hi Surfers, I have faced an issue with preproc-sess and I appreciate your help. I have a single slice EPI scan (number of TRs > 500; TR=0.2). When I tried to do preproc-sess, mc-afni2 is called and it crashed. When I checked the log, I noticed this: 3dvolreg.afni -verbose -dfile 005/fmcpr.mcdat -1Dmatrix_save 005/fmcpr.mat -base 005/tmp.mc-afni2.4869/tempvol.nii.gz -prefix 005/tmp.mc-afni2.4869/outvol.nii.gz 005/tmp.mc-afni2.4869/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2011_12_21_1014 (Aug 29 2012) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 005/tmp.mc-afni2.4869/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:005/tmp.mc-afni2.4869/tempvol.nii.gz is 30.100002 degrees from plumb. ++ Reading in base dataset 005/tmp.mc-afni2.4869/tempvol.nii.gz ++ Oblique dataset:005/tmp.mc-afni2.4869/invol.nii.gz is 30.100002 degrees from plumb. ++ Reading input dataset 005/tmp.mc-afni2.4869/invol.nii.gz ++ Edging: x=3 y=3 z=0 ++ Creating mask for -maxdisp + Automask has 847 voxels + 847 voxels left in -maxdisp mask after erosion ++ Initializing alignment base *** mri_3dalign_setup: cannot use nD images! ** Can't initialize base image for alignment ERROR: 3dvolreg.afni Invalid null command. Any suggestions? Please note that, this data is properly registered (manually and based on an auxiliary volume) and there is no problem there. Regards

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voxel wise cortical thickness and subcortical volume
by Zeng, Qi 29 Sep '20

29 Sep '20

External Email - Use Caution Hi, Is it possible to use Freesurfer to extract global voxel-wise cortical thickness and subcortical volume? Thank you so much! Best, Qi

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[WARNING: UNSCANNABLE EXTRACTION FAILED]RE: [EXTERNAL]Re: a question on Talairach transformation
by Yi Li 29 Sep '20

29 Sep '20

External Email - Use Caution Hi Douglas, I ran mri_convert --apply_transform talairach.xfm brainmask.mgz brainmask.talairach.mgz But brainmask.talairach.mgz is all black. No error was thrown during talairach transformation computation. Could you help to check what's going on here? I attached 4 relevant files in the mail. Thanks and best regards, Yi From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 1:33 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] [EXTERNAL]Re: a question on Talairach transformation Try mri_convert --apply_transform talairach.xfm brainmask.mgz brainmask.mni305.mgz On 9/15/2020 1:24 PM, Yi Li wrote: External Email - Use Caution Is there command in freesurfer that applies the linear transform (I suppose talairach.xfm) to brainmask.mgz to get the registered image? Best, Yi From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 1:20 PM To: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: [EXTERNAL]Re: [Freesurfer] a question on Talairach transformation No, it is in native individual space. We compute a linear transform but do not apply it On 9/15/2020 1:07 PM, Yi Li wrote: External Email - Use Caution Hi, I am a beginner of Freesurfer. I would be grateful if you could help me understand the excellent software. I got brainmask.mgz at the end of autorecon1 and brain.mgz in the middle of autorecon2. Are these the images registered to MNI305 template? In other words, is my understanding correct that brainmask.mgz is the image after orig.mgz is linearly registered to MNI305 (plus normalization and skullstripping), while brain.mgz is the image after normalized image is nonlinearly registered to MNI305 (plus cropping based on brainmask.mgz and further normalization)? Thank you so much for your help in advance. Best regards Yi Li --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible. --- The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.

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mri_surf2surf --projfrac error: cannot spec both --sval-xyz and --sval
by 谢娆 29 Sep '20

29 Sep '20

External Email - Use Caution Hi, To begin with, I want clarify my goal here: I want to resample my resting-state functional data in fsaverage5 and then do some preprocessing before statistical analysis, and I get stuck in smooth now. I tried the following command: mri_surf2surf --srcsubject sub-40 --srcsurfval /home/disk2/Data/HC/HCprep/derivatives/fmriprep/sub-40/ses-1/func/sub-40_ses-1_task-rest_run-1_space-fsnative_hemi-L_bold.func.gii --trgsubject fsaverage5 --trgicoorder 5 --trgsurfval /home/disk2/Data/HC/HCprep/sub-40_smooth6_proj.mgh --hemi lh --fwhm-trg 6 --projfrac white 0.5 --srcsubject: this is the freesurfer output folder from fmriprep (in ...derivatives/freesurfer/...) --srcsurfval: I used fmriprep --output-space fsnative to resample the resting data to subject native space. --trgsubject/--trgicoorder: I want to resample the data to a fsaverage5 as I mentioned before --projfrac white 0.5: I followed your advice to smooth use midthickness coordinates, but there is an error: ERROR: cannot spec both --sval-xyz and --sval then I tried to add these two parameters: mri_surf2surf --srcsubject sub-40 --srcsurfval /home/disk2/Data/HC/HCprep/derivatives/fmriprep/sub-40/ses-1/func/sub-40_ses-1_task-rest_run-1_space-fsnative_hemi-L_bold.func.gii --trgsubject fsaverage5 --trgicoorder 5 --trgsurfval /home/disk2/Data/HC/HCprep/sub-40_smooth6_proj.mgh --hemi lh --fwhm-trg 6 --projfrac white 0.5 --sval-xyz white --sval /home/disk2/Data/HC/HCprep/derivatives/fmriprep/sub-40/ses-1/func/ but the error still exist: ERROR: cannot spec both --sval-xyz and --sval I searched a lot but cannot found any useful help with it. I also have another question about smooth: I can also smooth my data with following command: mri_surf2surf --srcsubject fsaverage5 --srcsurfval /home/disk2/Data/HC/HCprep/derivatives/fmriprep/sub-15/ses-1/func/sub-15_ses-1_task-rest_run-1_space-fsaverage5_hemi-L_bold.func.gii --trgsubject fsaverage5 --trgsurfval /home/disk2/Data/HC/HCprep/sub-40_smooth6_proj.mgh --hemi lh --fwhm-trg 6 --projfrac white 0.5 (--projfrac didn't work here too) --srcsurfval: I used fmriprep --output-space fsaverage5 to resample the resting data to fsaverage5 in here With --srcsubject fsaverage5 specified here, will every subject use the same coordinate/distance info when performing smooth? Will the command I used above performing smooth using every subjects' own coordinate/distance info? And which command is better? Any help will be appreciated, Thanks a lot! rao

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Infant FreeSurfer
by k3ops＠free.fr 29 Sep '20

29 Sep '20

External Email - Use Caution Hi FreeSurfer team, I’ve been using the Infant FreeSurfer pipeline on 3DT1 sequences for few weeks now on infants from 0.4 to 5.4 years-old. I know Infant FreeSurfer is recommended for 0-2 years old infant but standard FreeSurfer was failing due to many lacunar infarcts in the white matter. So I tried Infant FreeSurfer with an age of 2 years old even for 2 to 5.4 years-old subjects and results look good. I know standard FreeSurfer has been tested on infant from 4.2 years-old, so what would be your recommendation for subjects from 2 to 4.2 years old? Have you already run Infant FreeSurfer on subjects older than 2 years-old? Do you recommend it? I also have some processing issues (see below) with my actual data: 1. Pixels with 0 value => probably out of the brainmask so the pixels are set to 0 after masking So, sometimes lateral ventricles are miss-segmented (see "pixel_0_brainmask" attachment) 2. Thalamus region is missing from the aseg stat export (always equal to 0 mm3), do you have a fix? Should I fix a LUT file? 3. Would it be possible to get the non-skullstripped N3 corrected 3D T1 in the MNI space (3D iso)? I was not able to find the registered 3DT1 to re-apply the N3 correction, I only found the input 3DT1 (mprage.nii.gz) in its native space. 4. Do you have any workaround for large ventricles segmentation issue (see "large_ventricles" attachment)? Standard FreeSurfer has a -bigventricle option, do you have a similar approach? And some additional questions: • brainstem seems to be split into multiple sub-regions, is it possible get the entire brainstem volume in the aseg stat export? • I saw that corpus callosum is not present in the “aseg” segmentation, so is this region out of the Infant FreeSurfer atlases? • Is it possible to get the mean cortical thickness for the labels you are providing? Many thanks as I know there are plenty of questions here :) Best, Florent

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Re: [Freesurfer] vol2surf: lesion overlap across group into surfaces
by Douglas N. Greve 28 Sep '20

28 Sep '20

The question is more for you. The lesions are not on the surface but you want to display them on the surface. How do you want to do that? ps. please remember to post to the list On 9/10/2020 10:25 AM, Horn, Mitchell Jacob wrote: > > Thanks so much Douglas. > > Many of the lesions are in the white matter, and many span across WM > and GM. In the case where the lesions on not strictly cortical, is > this surface mapping not possible? Or perhaps a representative surface > map showing the occurrences of lesions in any lobe/ROI? > > Best, > > Mitch >

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Freesurfer September 2020